Phages are the most abundant biological entities in the biosphere. Aside from their considerable impact on the planet’s ecology, evidence is emerging that phages have an important role in evolution. They are believed to be responsible for much of the lateral genetic transfer that occurs in microbial ecosystems and an important source of genetic diversity. However, viral evolution, the relations between the different groups of viruses and the impact of viruses on host evolution were largely unexplored areas in microbiology.
In the past we have worked on various aspects of the control gene expression in the phage T4 system and this eventually lead to an interest in phages that are evolutionarily distant from T4. The laboratory in Toulouse has a large collection of T4-type phages that infect a wide range of host bacteria (Shigella, Salmonella, Yersinia, Vibrios, Aeromonas, Burgholderia and Acinetobacter). Our group has previously carried out a systematic molecular analysis of this collection. The sequence comparisons of the major virion structural genes unambiguously demonstrated that all of these phages have diverged from a common ancestor as they infected new hosts and occupied novel ecological niches. Various subgroups of T4-type phages could be distinguished that are increasingly divergent from T4: the T-evens, the PseudoT-evens, the SchizoT-evens and the Exo-T-evens. Some key aspects of the virion morphology have changed during their evolution; for example, the SchizoT-even subgroup has a larger phage head and genome size than the other T4-type phage.
Although the 167 kb genome of T4 was sequenced a number of years ago, there was extremely little genomic sequence data on any of these other T4-type phages. However, the American NSF funded collaborative project with Prof. Jim Karam of Tulane Medical School for a high throughput genome sequencing project on ~15 diverse T4-like phages. This work is now nearly completed (http://phage.bioc.tulane.edu/) and we will briefly describe the genomes of only two of these phages that are both very different from T4 and from each other.
RB49 is an unusual T4-type coliphage. It is the one of the most distant T4-type coliphages analyzed. We have called such phages pseudoT-evens because of their phylogenetic divergence from T4. The other phage is Aeh1 that infects Aeromonas hydrophila, it has a longer head than T4 and thus a larger genome size (233234 bp). This phage, classified in the schizoT-even subgroup, appears to be even more phylogenetically distant from T4 than the pseudoT-even phages. The substantial preservation of genome content and gene order in T4, RB49 and Aeh1 demonstrates a common ancestry. These phages share ~90 genes with T4. In spite of some small re-arrangements, the gene order in the genome is essentially conserved. The most striking divergence in these genomes occurs within a region located between the T4 co-ordinates 45 kb and 75 kb. This segment is notably deprived of essential T4 genes and with the exception of a few enzymes (e.g. lysozyme and tk) nothing is conserved among the 3 genomes. In striking contrast, the adjacent virion structural module (~75 to 110 kb in T4) is highly conserved. Within this segment only a few sequences diverge significantly, most notably the C-terminal domains of the short tail spike fiber (g12) and collar fiber (gwac). However, a second, smaller virion structural module (~150-160 kb) encoding the major phage host range determinants, the long tail fibers and their adhesins, is extremely variable. In RB49 the adhesin gene g38 has been translocated to another location and in Aeh1 the homologues of the two T4 genes encoding the two distal parts of the tail fiber (g36 and g37) have been fused into a single gene that has then duplicated and diverged. Evidence has been previously presented that much of genetic diversity in this region has been created by recombinational shuffling within small regions of quasi-homology.